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Old 01-15-2019, 08:42 AM   #1
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Location: México

Join Date: Jan 2019
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Default Question: Metatranscriptome binning

Hi Everyone!

We work with a lignocellulose-degrading microbial consortia. Within a time-series experiment of an enriched culture, we perform a de novo crossassembly of metatranscriptome reads of four samples using SPAdes assembler and DIAMOND annotation, prior to differential expression analysis, we estimate the metabolic contribution of the individuals by recruitment of few bacterial genomes, surprisevely, there was five genomes almost totally covered by the RNA-seq data! and we decide try to perform a binning (MetaBAT) whit this data. One of the bins reached a 98% of completeness. It should be noted that RNA samples was treated with DNAse and RiboZero.
In your opionion, what could be the source of the sequences that contributed to these results? Is the effect by the algorithm more likely than some biological event difficult to circumvent such as the separation of operons in a non-synchronous culture?

Thanks a lot
GermoSG is offline   Reply With Quote
Old 01-16-2019, 11:25 AM   #2
Location: OH, USA

Join Date: Oct 2013
Posts: 18

I guess that the number of transcripts for that particular bacteria are more that they could cover 98% of their respective genome. If you do not expect this maybe you need to change the binning parameters.
Good luck!
rajarapupriya is offline   Reply With Quote

binning, de novo assembly, metagenome, metatranscriptomics

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